void *lammps_extract_compute(void *ptr, char *id, int style, int type)
{
LAMMPS *lmp = (LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id);
if (icompute < 0) return NULL;
Compute *compute = lmp->modify->compute[icompute];
if (style == 0) {
if (type == 0) {
if (!compute->scalar_flag) return NULL;
if (compute->invoked_scalar != lmp->update->ntimestep)
compute->compute_scalar();
return (void *) &compute->scalar;
}
if (type == 1) {
if (!compute->vector_flag) return NULL;
if (compute->invoked_vector != lmp->update->ntimestep)
compute->compute_vector();
return (void *) compute->vector;
}
if (type == 2) {
if (!compute->array_flag) return NULL;
if (compute->invoked_array != lmp->update->ntimestep)
compute->compute_array();
return (void *) compute->array;
}
}
if (style == 1) {
if (!compute->peratom_flag) return NULL;
if (type == 1) {
if (compute->invoked_peratom != lmp->update->ntimestep)
compute->compute_peratom();
return (void *) compute->vector_atom;
}
if (type == 2) {
if (compute->invoked_peratom != lmp->update->ntimestep)
compute->compute_peratom();
return (void *) compute->array_atom;
}
}
if (style == 2) {
if (!compute->local_flag) return NULL;
if (type == 1) {
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
return (void *) compute->vector_local;
}
if (type == 2) {
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
return (void *) compute->array_local;
}
}
return NULL;
}
void ComputeSlice::extract_one(int m, double *vec, int stride)
{
int i,j;
// invoke the appropriate compute if needed
if (which[m] == COMPUTE) {
Compute *compute = modify->compute[value2index[m]];
if (argindex[m] == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
double *cvector = compute->vector;
j = 0;
for (i = nstart; i < nstop; i += nskip) {
vec[j] = cvector[i-1];
j += stride;
}
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
double **carray = compute->array;
int icol = argindex[m]-1;
j = 0;
for (i = nstart; i < nstop; i += nskip) {
vec[j] = carray[i-1][icol];
j += stride;
}
}
// access fix fields, check if fix frequency is a match
} else if (which[m] == FIX) {
if (update->ntimestep % modify->fix[value2index[m]]->global_freq)
error->all(FLERR,"Fix used in compute slice not computed at compatible time");
Fix *fix = modify->fix[value2index[m]];
if (argindex[m] == 0) {
j = 0;
for (i = nstart; i < nstop; i += nskip) {
vec[j] = fix->compute_vector(i-1);
j += stride;
}
} else {
int icol = argindex[m]-1;
j = 0;
for (i = nstart; i < nstop; i += nskip) {
vec[j] = fix->compute_array(i-1,icol);
j += stride;
}
}
}
}
void FixAveHisto::end_of_step()
{
int i,j,m;
// skip if not step which requires doing something
// error check if timestep was reset in an invalid manner
bigint ntimestep = update->ntimestep;
if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep reset for fix ave/histo");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
// zero if first step
if (irepeat == 0) {
stats[0] = stats[1] = 0.0;
stats[2] = BIG;
stats[3] = -BIG;
for (i = 0; i < nbins; i++) bin[i] = 0.0;
}
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (i = 0; i < nvalues; i++) {
m = value2index[i];
j = argindex[i];
// atom attributes
if (which[i] == X)
bin_atoms(&atom->x[0][j],3);
else if (which[i] == V)
bin_atoms(&atom->v[0][j],3);
else if (which[i] == F)
bin_atoms(&atom->f[0][j],3);
// invoke compute if not previously invoked
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (kind == GLOBAL && mode == SCALAR) {
if (j == 0) {
if (!(compute->invoked_flag & INVOKED_SCALAR)) {
compute->compute_scalar();
compute->invoked_flag |= INVOKED_SCALAR;
}
bin_one(compute->scalar);
} else {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
bin_one(compute->vector[j-1]);
}
} else if (kind == GLOBAL && mode == VECTOR) {
if (j == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
bin_vector(compute->size_vector,compute->vector,1);
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
if (compute->array)
bin_vector(compute->size_array_rows,&compute->array[0][j-1],
compute->size_array_cols);
}
} else if (kind == PERATOM) {
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
}
if (j == 0)
bin_atoms(compute->vector_atom,1);
else if (compute->array_atom)
bin_atoms(&compute->array_atom[0][j-1],compute->size_peratom_cols);
} else if (kind == LOCAL) {
if (!(compute->invoked_flag & INVOKED_LOCAL)) {
compute->compute_local();
compute->invoked_flag |= INVOKED_LOCAL;
}
if (j == 0)
bin_vector(compute->size_local_rows,compute->vector_local,1);
else if (compute->array_local)
bin_vector(compute->size_local_rows,&compute->array_local[0][j-1],
compute->size_local_cols);
}
// access fix fields, guaranteed to be ready
} else if (which[i] == FIX) {
Fix *fix = modify->fix[m];
if (kind == GLOBAL && mode == SCALAR) {
if (j == 0) bin_one(fix->compute_scalar());
else bin_one(fix->compute_vector(j-1));
} else if (kind == GLOBAL && mode == VECTOR) {
if (j == 0) {
int n = fix->size_vector;
for (i = 0; i < n; i++) bin_one(fix->compute_vector(i));
} else {
int n = fix->size_vector;
for (i = 0; i < n; i++) bin_one(fix->compute_array(i,j-1));
}
} else if (kind == PERATOM) {
if (j == 0) bin_atoms(fix->vector_atom,1);
else if (fix->array_atom)
bin_atoms(fix->array_atom[j-1],fix->size_peratom_cols);
} else if (kind == LOCAL) {
if (j == 0) bin_vector(fix->size_local_rows,fix->vector_local,1);
else if (fix->array_local)
bin_vector(fix->size_local_rows,&fix->array_local[0][j-1],
fix->size_local_cols);
}
// evaluate equal-style variable
} else if (which[i] == VARIABLE && kind == GLOBAL) {
bin_one(input->variable->compute_equal(m));
} else if (which[i] == VARIABLE && kind == PERATOM) {
if (atom->nlocal > maxatom) {
memory->destroy(vector);
maxatom = atom->nmax;
memory->create(vector,maxatom,"ave/histo:vector");
}
input->variable->compute_atom(m,igroup,vector,1,0);
bin_atoms(vector,1);
}
}
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep + nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// merge histogram stats across procs if necessary
if (kind == PERATOM || kind == LOCAL) {
MPI_Allreduce(stats,stats_all,2,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&stats[2],&stats_all[2],1,MPI_DOUBLE,MPI_MIN,world);
MPI_Allreduce(&stats[3],&stats_all[3],1,MPI_DOUBLE,MPI_MAX,world);
MPI_Allreduce(bin,bin_all,nbins,MPI_DOUBLE,MPI_SUM,world);
stats[0] = stats_all[0];
stats[1] = stats_all[1];
stats[2] = stats_all[2];
stats[3] = stats_all[3];
for (i = 0; i < nbins; i++) bin[i] = bin_all[i];
}
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ave == ONE) {
stats_total[0] = stats[0];
stats_total[1] = stats[1];
stats_total[2] = stats[2];
stats_total[3] = stats[3];
for (i = 0; i < nbins; i++) bin_total[i] = bin[i];
} else if (ave == RUNNING) {
stats_total[0] += stats[0];
stats_total[1] += stats[1];
stats_total[2] = MIN(stats_total[2],stats[2]);
stats_total[3] = MAX(stats_total[3],stats[3]);
for (i = 0; i < nbins; i++) bin_total[i] += bin[i];
} else if (ave == WINDOW) {
stats_total[0] += stats[0];
if (window_limit) stats_total[0] -= stats_list[iwindow][0];
stats_list[iwindow][0] = stats[0];
stats_total[1] += stats[1];
if (window_limit) stats_total[1] -= stats_list[iwindow][1];
stats_list[iwindow][1] = stats[1];
if (window_limit) m = nwindow;
else m = iwindow+1;
stats_list[iwindow][2] = stats[2];
stats_total[2] = stats_list[0][2];
for (i = 1; i < m; i++)
stats_total[2] = MIN(stats_total[2],stats_list[i][2]);
stats_list[iwindow][3] = stats[3];
stats_total[3] = stats_list[0][3];
for (i = 1; i < m; i++)
stats_total[3] = MAX(stats_total[3],stats_list[i][3]);
for (i = 0; i < nbins; i++) {
bin_total[i] += bin[i];
if (window_limit) bin_total[i] -= bin_list[iwindow][i];
bin_list[iwindow][i] = bin[i];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
}
// output result to file
if (fp && me == 0) {
if (overwrite) fseek(fp,filepos,SEEK_SET);
fprintf(fp,BIGINT_FORMAT " %d %g %g %g %g\n",ntimestep,nbins,
stats_total[0],stats_total[1],stats_total[2],stats_total[3]);
if (stats_total[0] != 0.0)
for (i = 0; i < nbins; i++)
fprintf(fp,"%d %g %g %g\n",
i+1,coord[i],bin_total[i],bin_total[i]/stats_total[0]);
else
for (i = 0; i < nbins; i++)
fprintf(fp,"%d %g %g %g\n",i+1,coord[i],0.0,0.0);
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
ftruncate(fileno(fp),fileend);
}
}
}
void FixAveTime::invoke_vector(bigint ntimestep)
{
int i,j,m;
// zero if first step
if (irepeat == 0)
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array[i][j] = 0.0;
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (j = 0; j < nvalues; j++) {
m = value2index[j];
// invoke compute if not previously invoked
if (which[j] == COMPUTE) {
Compute *compute = modify->compute[m];
if (argindex[j] == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
double *cvector = compute->vector;
for (i = 0; i < nrows; i++)
column[i] = cvector[i];
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
double **carray = compute->array;
int icol = argindex[j]-1;
for (i = 0; i < nrows; i++)
column[i] = carray[i][icol];
}
// access fix fields, guaranteed to be ready
} else if (which[j] == FIX) {
Fix *fix = modify->fix[m];
if (argindex[j] == 0)
for (i = 0; i < nrows; i++)
column[i] = fix->compute_vector(i);
else {
int icol = argindex[j]-1;
for (i = 0; i < nrows; i++)
column[i] = fix->compute_array(i,icol);
}
}
// add columns of values to array or just set directly if offcol is set
if (offcol[j]) {
for (i = 0; i < nrows; i++)
array[i][j] = column[i];
} else {
for (i = 0; i < nrows; i++)
array[i][j] += column[i];
}
}
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep+nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// average the final result for the Nfreq timestep
double repeat = nrepeat;
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++)
if (offcol[j] == 0) array[i][j] /= repeat;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ntimestep >= startstep) {
if (ave == ONE) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array_total[i][j] = array[i][j];
norm = 1;
} else if (ave == RUNNING) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array_total[i][j] += array[i][j];
norm++;
} else if (ave == WINDOW) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) {
array_total[i][j] += array[i][j];
if (window_limit) array_total[i][j] -= array_list[iwindow][i][j];
array_list[iwindow][i][j] = array[i][j];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
if (window_limit) norm = nwindow;
else norm = iwindow;
}
}
// insure any columns with offcol set are effectively set to last value
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++)
if (offcol[j]) array_total[i][j] = norm*array[i][j];
// output result to file
if (fp && me == 0) {
fprintf(fp,BIGINT_FORMAT " %d\n",ntimestep,nrows);
for (i = 0; i < nrows; i++) {
fprintf(fp,"%d",i+1);
for (j = 0; j < nvalues; j++) fprintf(fp," %g",array_total[i][j]/norm);
fprintf(fp,"\n");
}
fflush(fp);
}
}
void FixAveTime::invoke_scalar(bigint ntimestep)
{
int i,m;
double scalar;
// zero if first step
if (irepeat == 0)
for (i = 0; i < nvalues; i++) vector[i] = 0.0;
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (i = 0; i < nvalues; i++) {
m = value2index[i];
// invoke compute if not previously invoked
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (argindex[i] == 0) {
if (!(compute->invoked_flag & INVOKED_SCALAR)) {
compute->compute_scalar();
compute->invoked_flag |= INVOKED_SCALAR;
}
scalar = compute->scalar;
} else {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
scalar = compute->vector[argindex[i]-1];
}
// access fix fields, guaranteed to be ready
} else if (which[i] == FIX) {
if (argindex[i] == 0)
scalar = modify->fix[m]->compute_scalar();
else
scalar = modify->fix[m]->compute_vector(argindex[i]-1);
// evaluate equal-style variable
} else if (which[i] == VARIABLE)
scalar = input->variable->compute_equal(m);
// add value to vector or just set directly if offcol is set
if (offcol[i]) vector[i] = scalar;
else vector[i] += scalar;
}
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep + nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// average the final result for the Nfreq timestep
double repeat = nrepeat;
for (i = 0; i < nvalues; i++)
if (offcol[i] == 0) vector[i] /= repeat;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ntimestep >= startstep) {
if (ave == ONE) {
for (i = 0; i < nvalues; i++) vector_total[i] = vector[i];
norm = 1;
} else if (ave == RUNNING) {
for (i = 0; i < nvalues; i++) vector_total[i] += vector[i];
norm++;
} else if (ave == WINDOW) {
for (i = 0; i < nvalues; i++) {
vector_total[i] += vector[i];
if (window_limit) vector_total[i] -= vector_list[iwindow][i];
vector_list[iwindow][i] = vector[i];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
if (window_limit) norm = nwindow;
else norm = iwindow;
}
}
// insure any columns with offcol set are effectively set to last value
for (i = 0; i < nvalues; i++)
if (offcol[i]) vector_total[i] = norm*vector[i];
// output result to file
if (fp && me == 0) {
fprintf(fp,BIGINT_FORMAT,ntimestep);
for (i = 0; i < nvalues; i++) fprintf(fp," %g",vector_total[i]/norm);
fprintf(fp,"\n");
fflush(fp);
}
}
void FixAveTime::invoke_vector(bigint ntimestep)
{
int i,j,m;
// first sample within single Nfreq epoch
// zero out arrays that accumulate over many samples, but not across epochs
// invoke setup_chunks() to determine current nchunk
// re-allocate per-chunk arrays if needed
// invoke lock() in two cases:
// if nrepeat > 1: so nchunk cannot change until Nfreq epoch is over,
// will be unlocked on last repeat of this Nfreq
// if ave = RUNNING/WINDOW and not yet locked:
// set forever, will be unlocked in fix destructor
// wrap setup_chunks in clearstep/addstep b/c it may invoke computes
// both nevery and nfreq are future steps,
// since call below to cchunk->ichunk()
// does not re-invoke internal cchunk compute on this same step
if (irepeat == 0) {
if (any_variable_length) {
modify->clearstep_compute();
int nrows_new = column_length(1);
modify->addstep_compute(ntimestep+nevery);
modify->addstep_compute(ntimestep+nfreq);
if (all_variable_length && nrows_new != nrows) {
nrows = nrows_new;
memory->destroy(column);
memory->create(column,nrows,"ave/time:column");
allocate_arrays();
}
bigint ntimestep = update->ntimestep;
int lockforever_flag = 0;
for (i = 0; i < nvalues; i++) {
if (!varlen[i]) continue;
if (nrepeat > 1 && ave == ONE) {
Compute *compute = modify->compute[value2index[i]];
compute->lock(this,ntimestep,ntimestep+(nrepeat-1)*nevery);
} else if ((ave == RUNNING || ave == WINDOW) && !lockforever) {
Compute *compute = modify->compute[value2index[i]];
compute->lock(this,update->ntimestep,-1);
lockforever_flag = 1;
}
}
if (lockforever_flag) lockforever = 1;
}
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array[i][j] = 0.0;
}
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (j = 0; j < nvalues; j++) {
m = value2index[j];
// invoke compute if not previously invoked
if (which[j] == COMPUTE) {
Compute *compute = modify->compute[m];
if (argindex[j] == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
double *cvector = compute->vector;
for (i = 0; i < nrows; i++)
column[i] = cvector[i];
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
double **carray = compute->array;
int icol = argindex[j]-1;
for (i = 0; i < nrows; i++)
column[i] = carray[i][icol];
}
// access fix fields, guaranteed to be ready
} else if (which[j] == FIX) {
Fix *fix = modify->fix[m];
if (argindex[j] == 0)
for (i = 0; i < nrows; i++)
column[i] = fix->compute_vector(i);
else {
int icol = argindex[j]-1;
for (i = 0; i < nrows; i++)
column[i] = fix->compute_array(i,icol);
}
}
// add columns of values to array or just set directly if offcol is set
if (offcol[j]) {
for (i = 0; i < nrows; i++)
array[i][j] = column[i];
} else {
for (i = 0; i < nrows; i++)
array[i][j] += column[i];
}
}
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep+nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// unlock any variable length computes at end of Nfreq epoch
// do not unlock if ave = RUNNING or WINDOW
if (any_variable_length && nrepeat > 1 && ave == ONE) {
for (i = 0; i < nvalues; i++) {
if (!varlen[i]) continue;
Compute *compute = modify->compute[value2index[i]];
compute->unlock(this);
}
}
// average the final result for the Nfreq timestep
double repeat = nrepeat;
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++)
if (offcol[j] == 0) array[i][j] /= repeat;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ave == ONE) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array_total[i][j] = array[i][j];
norm = 1;
} else if (ave == RUNNING) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array_total[i][j] += array[i][j];
norm++;
} else if (ave == WINDOW) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) {
array_total[i][j] += array[i][j];
if (window_limit) array_total[i][j] -= array_list[iwindow][i][j];
array_list[iwindow][i][j] = array[i][j];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
if (window_limit) norm = nwindow;
else norm = iwindow;
}
// insure any columns with offcol set are effectively set to last value
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++)
if (offcol[j]) array_total[i][j] = norm*array[i][j];
// output result to file
if (fp && me == 0) {
if (overwrite) fseek(fp,filepos,SEEK_SET);
fprintf(fp,BIGINT_FORMAT " %d\n",ntimestep,nrows);
for (i = 0; i < nrows; i++) {
fprintf(fp,"%d",i+1);
for (j = 0; j < nvalues; j++) fprintf(fp,format,array_total[i][j]/norm);
fprintf(fp,"\n");
}
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
if (fileend > 0) ftruncate(fileno(fp),fileend);
}
}
}
void FixAveTime::invoke_scalar(bigint ntimestep)
{
int i,m;
double scalar;
// zero if first sample within single Nfreq epoch
// NOTE: doc this
// are not checking for returned length, just initialize it
// check for exceeding length is done below
if (irepeat == 0) {
if (any_variable_length) {
modify->clearstep_compute();
column_length(1);
modify->addstep_compute(ntimestep+nevery);
modify->addstep_compute(ntimestep+nfreq);
}
for (i = 0; i < nvalues; i++) vector[i] = 0.0;
}
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (i = 0; i < nvalues; i++) {
m = value2index[i];
// invoke compute if not previously invoked
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (argindex[i] == 0) {
if (!(compute->invoked_flag & INVOKED_SCALAR)) {
compute->compute_scalar();
compute->invoked_flag |= INVOKED_SCALAR;
}
scalar = compute->scalar;
} else {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
// insure no out-of-range access to variable-length compute vector
if (varlen[i] && compute->size_vector < argindex[i]) scalar = 0.0;
else scalar = compute->vector[argindex[i]-1];
}
// access fix fields, guaranteed to be ready
} else if (which[i] == FIX) {
if (argindex[i] == 0)
scalar = modify->fix[m]->compute_scalar();
else
scalar = modify->fix[m]->compute_vector(argindex[i]-1);
// evaluate equal-style variable
} else if (which[i] == VARIABLE)
scalar = input->variable->compute_equal(m);
// add value to vector or just set directly if offcol is set
if (offcol[i]) vector[i] = scalar;
else vector[i] += scalar;
}
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep + nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// average the final result for the Nfreq timestep
double repeat = nrepeat;
for (i = 0; i < nvalues; i++)
if (offcol[i] == 0) vector[i] /= repeat;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ave == ONE) {
for (i = 0; i < nvalues; i++) vector_total[i] = vector[i];
norm = 1;
} else if (ave == RUNNING) {
for (i = 0; i < nvalues; i++) vector_total[i] += vector[i];
norm++;
} else if (ave == WINDOW) {
for (i = 0; i < nvalues; i++) {
vector_total[i] += vector[i];
if (window_limit) vector_total[i] -= vector_list[iwindow][i];
vector_list[iwindow][i] = vector[i];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
if (window_limit) norm = nwindow;
else norm = iwindow;
}
// insure any columns with offcol set are effectively set to last value
for (i = 0; i < nvalues; i++)
if (offcol[i]) vector_total[i] = norm*vector[i];
// output result to file
if (fp && me == 0) {
clearerr(fp);
if (overwrite) fseek(fp,filepos,SEEK_SET);
fprintf(fp,BIGINT_FORMAT,ntimestep);
for (i = 0; i < nvalues; i++) fprintf(fp,format,vector_total[i]/norm);
fprintf(fp,"\n");
if (ferror(fp))
error->one(FLERR,"Error writing out time averaged data");
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
if (fileend > 0) ftruncate(fileno(fp),fileend);
}
}
}
void ComputeChunkSpreadAtom::compute_peratom()
{
invoked_peratom = update->ntimestep;
// grow local vector_atom or array_atom if necessary
if (atom->nmax > nmax) {
if (nvalues == 1) {
memory->destroy(vector_atom);
nmax = atom->nmax;
memory->create(vector_atom,nmax,"chunk/spread/atom:vector_atom");
} else {
memory->destroy(array_atom);
nmax = atom->nmax;
memory->create(array_atom,nmax,nvalues,"chunk/spread/atom:array_atom");
}
}
// compute chunk/atom assigns atoms to chunk IDs
// extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
int nchunk = cchunk->setup_chunks();
cchunk->compute_ichunk();
int *ichunk = cchunk->ichunk;
// loop over values, access compute or fix
// loop over atoms, use chunk ID of each atom to store value from compute/fix
int *mask = atom->mask;
int nlocal = atom->nlocal;
int i,m,n,index,nstride;
double *ptr;
for (m = 0; m < nvalues; m++) {
n = value2index[m];
// copy compute/fix values into vector_atom or array_atom
// nstride between values for each atom
if (nvalues == 1) {
ptr = vector_atom;
nstride = 1;
} else {
ptr = &array_atom[0][m];
nstride = nvalues;
}
// invoke compute if not previously invoked
if (which[m] == COMPUTE) {
Compute *compute = modify->compute[n];
if (argindex[m] == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
double *cvector = compute->vector;
for (i = 0; i < nlocal; i++, ptr += nstride) {
*ptr = 0.0;
if (!(mask[i] & groupbit)) continue;
index = ichunk[i]-1;
if (index < 0 || index >= nchunk) continue;
*ptr = cvector[index];
}
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
int icol = argindex[m]-1;
double **carray = compute->array;
for (i = 0; i < nlocal; i++, ptr += nstride) {
*ptr = 0.0;
if (!(mask[i] & groupbit)) continue;
index = ichunk[i]-1;
if (index < 0 || index >= nchunk) continue;
*ptr = carray[index][icol];
}
}
// access fix data, check if fix frequency is a match
// are assuming the fix global vector/array is per-chunk data
// check if index exceeds fix output length/rows
} else if (which[m] == FIX) {
Fix *fix = modify->fix[n];
if (update->ntimestep % fix->global_freq)
error->all(FLERR,"Fix used in compute chunk/spread/atom not "
"computed at compatible time");
if (argindex[m] == 0) {
int nfix = fix->size_vector;
for (i = 0; i < nlocal; i++, ptr += nstride) {
*ptr = 0.0;
if (!(mask[i] & groupbit)) continue;
index = ichunk[i]-1;
if (index < 0 || index >= nchunk || index >= nfix) continue;
*ptr = fix->compute_vector(index);
}
} else {
int icol = argindex[m]-1;
int nfix = fix->size_array_rows;
for (i = 0; i < nlocal; i++, ptr += nstride) {
*ptr = 0.0;
if (!(mask[i] & groupbit)) continue;
index = ichunk[i]-1;
if (index < 0 || index >= nchunk || index >= nfix) continue;
*ptr = fix->compute_array(index,icol);
}
}
}
}
}
void FixAveCorrelate::end_of_step()
{
int i,j,m;
double scalar;
// skip if not step which requires doing something
// error check if timestep was reset in an invalid manner
bigint ntimestep = update->ntimestep;
if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep reset for fix ave/correlate");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
// accumulate results of computes,fixes,variables to origin
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
// lastindex = index in values ring of latest time sample
lastindex++;
if (lastindex == nrepeat) lastindex = 0;
for (i = 0; i < nvalues; i++) {
m = value2index[i];
// invoke compute if not previously invoked
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (argindex[i] == 0) {
if (!(compute->invoked_flag & INVOKED_SCALAR)) {
compute->compute_scalar();
compute->invoked_flag |= INVOKED_SCALAR;
}
scalar = compute->scalar;
} else {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
scalar = compute->vector[argindex[i]-1];
}
// access fix fields, guaranteed to be ready
} else if (which[i] == FIX) {
if (argindex[i] == 0)
scalar = modify->fix[m]->compute_scalar();
else
scalar = modify->fix[m]->compute_vector(argindex[i]-1);
// evaluate equal-style variable
} else if (which[i] == VARIABLE)
scalar = input->variable->compute_equal(m);
values[lastindex][i] = scalar;
}
// fistindex = index in values ring of earliest time sample
// nsample = number of time samples in values ring
if (nsample < nrepeat) nsample++;
else {
firstindex++;
if (firstindex == nrepeat) firstindex = 0;
}
nvalid += nevery;
modify->addstep_compute(nvalid);
// calculate all Cij() enabled by latest values
accumulate();
if (ntimestep % nfreq) return;
// save results in save_count and save_corr
for (i = 0; i < nrepeat; i++) {
save_count[i] = count[i];
if (count[i])
for (j = 0; j < npair; j++)
save_corr[i][j] = prefactor*corr[i][j]/count[i];
else
for (j = 0; j < npair; j++)
save_corr[i][j] = 0.0;
}
// output result to file
if (fp && me == 0) {
if (overwrite) fseek(fp,filepos,SEEK_SET);
fprintf(fp,BIGINT_FORMAT " %d\n",ntimestep,nrepeat);
for (i = 0; i < nrepeat; i++) {
fprintf(fp,"%d %d %d",i+1,i*nevery,count[i]);
if (count[i])
for (j = 0; j < npair; j++)
fprintf(fp," %g",prefactor*corr[i][j]/count[i]);
else
for (j = 0; j < npair; j++)
fprintf(fp," 0.0");
fprintf(fp,"\n");
}
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
ftruncate(fileno(fp),fileend);
}
}
// zero accumulation if requested
// recalculate Cij(0)
if (ave == ONE) {
for (i = 0; i < nrepeat; i++) {
count[i] = 0;
for (j = 0; j < npair; j++)
corr[i][j] = 0.0;
}
nsample = 1;
accumulate();
}
}
void FixSAEDVTK::invoke_vector(bigint ntimestep)
{
// zero if first step
int icompute = modify->find_compute(ids);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix saed/vtk does not exist");
if (irepeat == 0)
for (int i = 0; i < nrows; i++)
vector[i] = 0.0;
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
// invoke compute if not previously invoked
Compute *compute = modify->compute[icompute];
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
double *vector = compute->vector;
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep+nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// average the final result for the Nfreq timestep
double repeat = nrepeat;
for ( int i = 0; i < nrows; i++)
vector[i] /= repeat;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ave == ONE) {
for (int i = 0; i < nrows; i++) vector_total[i] = vector[i];
norm = 1;
} else if (ave == RUNNING) {
for (int i = 0; i < nrows; i++) vector_total[i] += vector[i];
norm++;
} else if (ave == WINDOW) {
for (int i = 0; i < nrows; i++) {
vector_total[i] += vector[i];
if (window_limit) vector_total[i] -= vector_list[iwindow][i];
vector_list[iwindow][i] = vector[i];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
if (window_limit) norm = nwindow;
else norm = iwindow;
}
// output result to file
if (fp && me == 0) {
if (nOutput > 0) {
fclose(fp);
char nName [128];
sprintf(nName,"%s.%d.vtk",filename,nOutput);
fp = fopen(nName,"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix saed/vtk file %s",nName);
error->one(FLERR,str);
}
}
fprintf(fp,"# vtk DataFile Version 3.0 c_%s\n",ids);
fprintf(fp,"Image data set\n");
fprintf(fp,"ASCII\n");
fprintf(fp,"DATASET STRUCTURED_POINTS\n");
fprintf(fp,"DIMENSIONS %d %d %d\n", Dim[0], Dim[1], Dim[2]);
fprintf(fp,"ASPECT_RATIO %g %g %g\n", dK[0], dK[1], dK[2]);
fprintf(fp,"ORIGIN %g %g %g\n", Knmin[0] * dK[0], Knmin[1] * dK[1], Knmin[2] * dK[2]);
fprintf(fp,"POINT_DATA %d\n", Dim[0] * Dim[1] * Dim[2] );
fprintf(fp,"SCALARS intensity float\n");
fprintf(fp,"LOOKUP_TABLE default\n");
filepos = ftell(fp);
if (overwrite) fseek(fp,filepos,SEEK_SET);
// Finding the intersection of the reciprical space and Ewald sphere
int NROW1 = 0;
int NROW2 = 0;
double dinv2 = 0.0;
double r = 0.0;
double K[3];
// Zone flag to capture entire recrocal space volume
if ( (Zone[0] == 0) && (Zone[1] == 0) && (Zone[2] == 0) ){
for (int k = Knmin[2]; k <= Knmax[2]; k++) {
for (int j = Knmin[1]; j <= Knmax[1]; j++) {
for (int i = Knmin[0]; i <= Knmax[0]; i++) {
K[0] = i * dK[0];
K[1] = j * dK[1];
K[2] = k * dK[2];
dinv2 = (K[0] * K[0] + K[1] * K[1] + K[2] * K[2]);
if (dinv2 < Kmax * Kmax) {
fprintf(fp,"%g\n",vector_total[NROW1]/norm);
fflush(fp);
NROW1++;
NROW2++;
} else {
fprintf(fp,"%d\n",-1);
fflush(fp);
NROW2++;
}
}
}
}
} else {
for (int k = Knmin[2]; k <= Knmax[2]; k++) {
for (int j = Knmin[1]; j <= Knmax[1]; j++) {
for (int i = Knmin[0]; i <= Knmax[0]; i++) {
K[0] = i * dK[0];
K[1] = j * dK[1];
K[2] = k * dK[2];
dinv2 = (K[0] * K[0] + K[1] * K[1] + K[2] * K[2]);
if (dinv2 < Kmax * Kmax) {
r=0.0;
for (int m=0; m<3; m++) r += pow(K[m] - Zone[m],2.0);
r = sqrt(r);
if ( (r > (R_Ewald - dR_Ewald) ) && (r < (R_Ewald + dR_Ewald) ) ){
fprintf(fp,"%g\n",vector_total[NROW1]/norm);
fflush(fp);
NROW2++;
NROW1++;
} else {
fprintf(fp,"%d\n",-1);
fflush(fp);
NROW2++;
}
} else {
fprintf(fp,"%d\n",-1);
fflush(fp);
NROW2++;
}
}
}
}
}
}
nOutput++;
}
void FixAveTimeSAED::invoke_vector(bigint ntimestep)
{
int i,j,m;
// zero if first step
if (irepeat == 0)
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array[i][j] = 0.0;
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (j = 0; j < nvalues; j++) {
m = value2index[j];
// invoke compute if not previously invoked
if (which[j] == COMPUTE) {
Compute *compute = modify->compute[m];
if (argindex[j] == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
double *cvector = compute->vector;
for (i = 0; i < nrows; i++)
column[i] = cvector[i];
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
double **carray = compute->array;
int icol = argindex[j]-1;
for (i = 0; i < nrows; i++)
column[i] = carray[i][icol];
}
}
// add columns of values to array or just set directly if offcol is set
if (offcol[j]) {
for (i = 0; i < nrows; i++)
array[i][j] = column[i];
} else {
for (i = 0; i < nrows; i++)
array[i][j] += column[i];
}
}
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep+nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// average the final result for the Nfreq timestep
double repeat = nrepeat;
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++)
if (offcol[j] == 0) array[i][j] /= repeat;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ave == ONE) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array_total[i][j] = array[i][j];
norm = 1;
} else if (ave == RUNNING) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array_total[i][j] += array[i][j];
norm++;
} else if (ave == WINDOW) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) {
array_total[i][j] += array[i][j];
if (window_limit) array_total[i][j] -= array_list[iwindow][i][j];
array_list[iwindow][i][j] = array[i][j];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
if (window_limit) norm = nwindow;
else norm = iwindow;
}
// insure any columns with offcol set are effectively set to last value
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++)
if (offcol[j]) array_total[i][j] = norm*array[i][j];
// output result to file
if (fp && me == 0) {
if (nOutput > 0) {
fclose(fp);
char nName [128];
sprintf(nName,"%s.%d.vtk",filename,nOutput);
fp = fopen(nName,"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix ave/time file %s",nName);
error->one(FLERR,str);
}
}
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
fprintf(fp,"# vtk DataFile Version 3.0 c_%s\n",ids[i]);
fprintf(fp,"Image data set\n");
fprintf(fp,"ASCII\n");
fprintf(fp,"DATASET STRUCTURED_POINTS\n");
fprintf(fp,"DIMENSIONS %d %d %d\n", Dim[0], Dim[1], Dim[2]);
fprintf(fp,"ASPECT_RATIO %g %g %g\n", dK[0], dK[1], dK[2]);
fprintf(fp,"ORIGIN %g %g %g\n", Knmin[0] * dK[0], Knmin[1] * dK[1], Knmin[2] * dK[2]);
fprintf(fp,"POINT_DATA %d\n", Dim[0] * Dim[1] * Dim[2] );
fprintf(fp,"SCALARS intensity float\n");
fprintf(fp,"LOOKUP_TABLE default\n");
} else break;
if (argindex[i]) fprintf(fp,"[%d]",argindex[i]);
}
filepos = ftell(fp);
if (overwrite) fseek(fp,filepos,SEEK_SET);
// Finding the intersection of the reciprical space and Ewald sphere
int NROW1 = 0;
int NROW2 = 0;
double dinv2 = 0.0;
double r = 0.0;
double K[3];
// Zone flag to capture entire recrocal space volume
if ( (Zone[0] == 0) && (Zone[1] == 0) && (Zone[2] == 0) ){
for (int k = Knmin[2]; k <= Knmax[2]; k++) {
for (int j = Knmin[1]; j <= Knmax[1]; j++) {
for (int i = Knmin[0]; i <= Knmax[0]; i++) {
K[0] = i * dK[0];
K[1] = j * dK[1];
K[2] = k * dK[2];
dinv2 = (K[0] * K[0] + K[1] * K[1] + K[2] * K[2]);
if (dinv2 < Kmax * Kmax) {
fprintf(fp,"%g\n",array_total[NROW1][0]/norm);
fflush(fp);
NROW1++;
NROW2++;
} else {
fprintf(fp,"%d\n",-1);
fflush(fp);
NROW2++;
}
}
}
}
} else {
for (int k = Knmin[2]; k <= Knmax[2]; k++) {
for (int j = Knmin[1]; j <= Knmax[1]; j++) {
for (int i = Knmin[0]; i <= Knmax[0]; i++) {
K[0] = i * dK[0];
K[1] = j * dK[1];
K[2] = k * dK[2];
dinv2 = (K[0] * K[0] + K[1] * K[1] + K[2] * K[2]);
if (dinv2 < Kmax * Kmax) {
r=0.0;
for (int m=0; m<3; m++) r += pow(K[m] - Zone[m],2.0);
r = sqrt(r);
if ( (r > (R_Ewald - dR_Ewald) ) && (r < (R_Ewald + dR_Ewald) ) ){
fprintf(fp,"%g\n",array_total[NROW1][0]/norm);
fflush(fp);
NROW2++;
NROW1++;
} else {
fprintf(fp,"%d\n",-1);
fflush(fp);
NROW2++;
}
} else {
fprintf(fp,"%d\n",-1);
fflush(fp);
NROW2++;
}
}
}
}
}
if (me == 0) { if (screen)cout << " FIX AVE TIME SAED ---- n = " << NROW1 << endl; }
}
nOutput++;
}
